MDAnalysis command line interface

mdacli is a simple command line interface (CLI) to the analysis classes of MDAnalysis using argparse. Contributions are welcome!

To install mdacli refer to the INSTALL file.

Run mdacli:

mda -h

For a help and an overview of the supported modules. A help message for each module is available using:

mda <module> -h

Available modules

Currently the following analysis modules are available

Module Name	Description
AlignTraj	RMS-align trajectory to a reference structure using a selection.
AverageStructure	RMS-align trajectory to a reference structure using a selection, and calculate the average coordinates of the trajectory.
Contacts	Calculate contacts based observables.
DensityAnalysis	Volumetric density analysis.
DistanceMatrix	Calculate the pairwise distance between each frame in a trajectory
Dihedral	Calculate dihedral angles for specified atomgroups.
Janin	Calculate χ_1 and χ_2 dihedral angles of selected group
Ramachandran	Calculate ϕ and ψ dihedral angles of selected group
DielectricConstant	Computes the average dipole moment.
GNMAnalysis	Basic tool for GNM analysis.
closeContactGNMAnalysis	GNMAnalysis only using close contacts.
HELANAL	Perform HELANAL helix analysis on your trajectory.
HoleAnalysis	Run hole program on a trajectory.
LinearDensity	Linear density profile
EinsteinMSD	Class to calculate Mean Squared Displacement by the Einstein relation.
PCA	Principal component analysis on an MD trajectory.
InterRDF	Intermolecular pair distribution function
RMSD	Class to perform RMSD analysis on a trajectory.
RMSF	Calculate RMSF of given atoms across a trajectory.

More information about each module is available through the help page or at the MDAnalysis documentation.

Metadata

Release files for mdacli 0.1.33

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for mdacli 0.1.33
File	Size	Uploaded
mdacli-0.1.33.tar.gz	39.3 kB	Oct 20, 2025	Details

Built distribution (wheel)

Table of built distributions (wheels) for mdacli 0.1.33
File	Interpreter	ABI	Platform	Reset
mdacli-0.1.33-py3-none-any.whl 36.8 kB Oct 20, 2025	Python 3	none	any	Details

Total release size: 76.1 kB

Release files / mdacli-0.1.33.tar.gz

Download URL	mdacli-0.1.33.tar.gz
Size	39.3 kB
Tags	Source
SHA-256 checksum How to use checksums	`3fe8e5e0abf594a5992c1682d3a19b3fea6b5cbf79037c11cb0528a2ea1f930c`
BLAKE2b-256 checksum How to use checksums	`9e34e14c67c931461cf5b2627151d685f30082c5589d1c79ce18470b0c9ba93c`
Upload date	Oct 20, 2025
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/6.1.0 CPython/3.13.7`

Provenance

Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/MDAnalysis/mdacli
Publishing commit: github.com/MDAnalysis/mdacli/tree/d5917df7054ed6ab7dea317da8951843f886b0e7

Workflow

Publishing configuration: github.com/MDAnalysis/mdacli/blob/d5917df7054ed6ab7dea317da8951843f886b0e7/.github/workflows/release.yml
Publishing logs: github.com/MDAnalysis/mdacli/actions/runs/18655962392/attempts/1

Artifact

Subject: mdacli-0.1.33.tar.gz
SHA-256 checksum: 3fe8e5e0abf594a5992c1682d3a19b3fea6b5cbf79037c11cb0528a2ea1f930c Verifying attestations

Release files / mdacli-0.1.33-py3-none-any.whl

Download URL	mdacli-0.1.33-py3-none-any.whl
Size	36.8 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`97d77b8eca27d139147aa894d07572b814137987105dabcc9a6692d8da290e50`
BLAKE2b-256 checksum How to use checksums	`8d795a9b4a6a0a773fab4a633b9274632c2ae252d66073899bdb045498eda4d1`
Upload date	Oct 20, 2025
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/6.1.0 CPython/3.13.7`

Provenance

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/MDAnalysis/mdacli
Publishing commit: github.com/MDAnalysis/mdacli/tree/d5917df7054ed6ab7dea317da8951843f886b0e7

Workflow

Publishing configuration: github.com/MDAnalysis/mdacli/blob/d5917df7054ed6ab7dea317da8951843f886b0e7/.github/workflows/release.yml
Publishing logs: github.com/MDAnalysis/mdacli/actions/runs/18655962392/attempts/1

Artifact

Subject: mdacli-0.1.33-py3-none-any.whl
SHA-256 checksum: 97d77b8eca27d139147aa894d07572b814137987105dabcc9a6692d8da290e50 Verifying attestations